idef.h File Reference

#include <cstdio>
#include <array>
#include <vector>
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/real.h"

Include dependency graph for idef.h:

This graph shows which files directly or indirectly include this file:

Description

Defines interaction types and parameters.

Classes
union	t_iparams
	Union of various interaction paramters. More...
struct	InteractionList
	List of listed interactions. More...
struct	t_ilist
	Deprecated list of listed interactions. More...
struct	InteractionListHandle
	Type for returning a list of InteractionList references. More...
struct	gmx_cmapdata_t
	CMAP data for a single grid. More...
struct	gmx_cmap_t
	CMAP grids. More...
class	InteractionDefinitions
	Struct with list of interaction parameters and lists of interactions. More...
struct	t_idef
	Deprecated interation definitions, used in t_topology. More...

Typedefs
typedef union t_iparams	t_iparams
	Union of various interaction paramters. More...
typedef int	t_functype
using	InteractionLists = std::array< InteractionList, F_NRE >
	List of interaction lists. More...

Enumerations
enum	{ ilsortUNKNOWN, ilsortNO_FE, ilsortFE_SORTED }
	Sorting of the interaction list. More...

Functions
static std::vector < InteractionListHandle >	extractILists (const InteractionLists &ilists, int flags)
	Returns a list of all non-empty InteractionList entries with any of the interaction flags in flags set. More...
static int	ilistStride (const InteractionListHandle &ilistHandle)
	Returns the stride for the iatoms array in ilistHandle. More...
void	printInteractionParameters (gmx::TextWriter *writer, t_functype ftype, const t_iparams &iparams)
void	pr_iparams (FILE *fp, t_functype ftype, const t_iparams &iparams)
void	pr_ilist (FILE *fp, int indent, const char *title, const t_functype *functype, const InteractionList &ilist, bool bShowNumbers, bool bShowParameters, const t_iparams *iparams)
void	pr_idef (FILE *fp, int indent, const char *title, const t_idef *idef, bool bShowNumbers, bool bShowParameters)
void	init_idef (t_idef *idef)
	Properly initialize idef struct. More...
void	done_idef (t_idef *idef)
	Properly clean up idef struct. More...

Typedef Documentation

using InteractionLists = std::array<InteractionList, F_NRE>

List of interaction lists.

Contains one list for each interaction type.

TODO: Consider only including entries in use instead of all F_NRE

typedef union t_iparams t_iparams

Union of various interaction paramters.

Some parameters have A and B values for free energy calculations. The B values are not used for regular simulations of course. Free Energy for nonbondeds can be computed by changing the atom type. The harmonic type is used for all harmonic potentials: bonds, angles and improper dihedrals.

No free energy supported for cubic bonds, FENE, WPOL or cross terms.

Enumeration Type Documentation

anonymous enum

Sorting of the interaction list.

Enumerator
ilsortUNKNOWN	Sorting unknown.
ilsortNO_FE	Sorting without the free energy interactions.
ilsortFE_SORTED	Sorting with the free energy interactions also sorted.

Function Documentation

void done_idef

(

t_idef *

idef

)

Properly clean up idef struct.

Parameters

[in]

idef

Pointer to idef struct to clean up.

static std::vector<InteractionListHandle> extractILists ( const InteractionLists &  ilists, int  flags  )

inlinestatic

Returns a list of all non-empty InteractionList entries with any of the interaction flags in flags set.

Parameters

[in]	ilists	Set of interaction lists.
[in]	flags	Bit mask with one or more IF_... bits set.

static int ilistStride ( const InteractionListHandle &  ilistHandle )

inlinestatic

Returns the stride for the iatoms array in ilistHandle.

Parameters

[in]

ilistHandle

The ilist to return the stride for.

void init_idef

(

t_idef *

idef

)

Properly initialize idef struct.

Parameters

[in]

idef

Pointer to idef struct to initialize.